Locus 3335

Sequence ID	3L_DroMel_CAF1
Location	9,800,918 – 9,801,049
Length	131
Max. P	0.989759

overview

Window 0

Location	9,800,918 – 9,801,033
Length	115
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	76.49
Mean single sequence MFE	-26.31
Consensus MFE	-9.44
Energy contribution	-8.96
Covariance contribution	-0.48
Combinations/Pair	1.39
Mean z-score	-2.55
Structure conservation index	0.36
SVM decision value	2.18
SVM RNA-class probability	0.989759
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9800918 115 - 23771897
ACCGCAUCCGCAUCCUUUGUAAGAUCUGCUGGGGCUUCACUAGUACCCAAAUCUUUUUUACUCUCUUUUUGGAUAGCUGAUUUGUCUUCCAC---CAACUCCUCUUUGGAUGCUGCUA
...(((...((((((...((((((.....(((((((.....))).))))......))))))........((((..((......))..)))).---............))))))))).. ( -28.00)
>DroSec_CAF1 95444 112 - 1
UCU---UCCGAACACUUUGUAAGAUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUAUCUUUUUGGAUAGCUGGUUUGUCUUCCAG---CAACUCAUCUUUGGAAGGUGAUU
(((---(((((((.....))..((..(((((.(((...((((((..(((((................)))))...))))))..)))...)))---))..))....))))))))..... ( -28.99)
>DroSim_CAF1 98223 100 - 1
ACU---GCCGC------------AUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUAUCUUUUUGGAUAGCUGGUUUGUCUUCCAG---CAACUCAUCUUUGGAAGGUGAUA
...---(((((------------(.....))))))...((((((..(((((................)))))...))))))(..((((((((---..........))))))))..).. ( -27.69)
>DroEre_CAF1 97309 112 - 1
ACU---UCCGCAUCCUUUGCAAGAUCUGCCUUGGCCUCCAUGGCAUCCAAAUCUUUUCCACUCUCUUUUUGGAUAGCUGGUUUGUCUUCCAC---CAACUCCUUUUUGGCUGGUGAUA
...---...(((.....)))(((((..(((...(((.....)))(((((((................)))))))....)))..))))).(((---((...((.....)).)))))... ( -27.99)
>DroYak_CAF1 107498 115 - 1
CCU---UCUGCUUCCUUUGUGAGAUCUUCUUUGGCUUCACUUGCACCCAAAUCUUUGCCACUCUCUUUUAGGAUAGAUACCUUUUCUUCUUCCCGUAAAUCUUGUUUGGCUGGUGACA
...---............(((((..(......)..))))).((((((.........((((..(...((((((..(((..........)))..)).))))....)..)))).)))).)) ( -18.90)
>consensus
ACU___UCCGCAUCCUUUGUAAGAUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUCUCUUUUUGGAUAGCUGGUUUGUCUUCCAC___CAACUCAUCUUUGGAUGGUGAUA
.......((...........(((((.((.....(((.....)))...)).)))))..............((((..((......))..))))................))......... ( -9.44 =  -8.96 +  -0.48)

alignment

secondary structure

dotplot

Window 1

Location	9,800,955 – 9,801,049
Length	94
Sequences	4
Columns	94
Reading direction	reverse
Mean pairwise identity	79.46
Mean single sequence MFE	-16.27
Consensus MFE	-8.30
Energy contribution	-8.49
Covariance contribution	0.19
Combinations/Pair	1.15
Mean z-score	-2.61
Structure conservation index	0.51
SVM decision value	0.78
SVM RNA-class probability	0.849166
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9800955 94 - 23771897
UCUCUCCGUUUCCUCCACCGCAUCCGCAUCCUUUGUAAGAUCUGCUGGGGCUUCACUAGUACCCAAAUCUUUUUUACUCUCUUUUUGGAUAGCU
...................(((((((........((((((.....(((((((.....))).))))......))))))........))))).)). ( -17.09)
>DroSec_CAF1 95481 91 - 1
UCUGUCCGUUGCUUCCUCU---UCCGAACACUUUGUAAGAUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUAUCUUUUUGGAUAGCU
.(((((((........(((---(.(((.....))).))))..(((((((....))).))))........................))))))).. ( -15.60)
>DroSim_CAF1 98260 79 - 1
UCUGUCCCUUUCCUCCACU---GCCGC------------AUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUAUCUUUUUGGAUAGCU
...................---(((((------------(.....)))))).........................((((((....)))))).. ( -13.70)
>DroEre_CAF1 97346 91 - 1
UCUGUCCUUUUCCUCCACU---UCCGCAUCCUUUGCAAGAUCUGCCUUGGCCUCCAUGGCAUCCAAAUCUUUUCCACUCUCUUUUUGGAUAGCU
.((((((............---...(((.....)))(((((.((((.(((...))).)))).....)))))...............)))))).. ( -18.70)
>consensus
UCUGUCCGUUUCCUCCACU___UCCGCAUCCUUUGUAAGAUCUGCUGUGGCUUCACUAGCACCCAAAUCUUUUUUACUAUCUUUUUGGAUAGCU
...........................................(((((.(((.....)))..(((((................)))))))))). ( -8.30 =  -8.49 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:55:04 2006